The last method of flats fishing with a kayak is the least known or practiced. This method is trolling, I am not sure if I have ever shared this on Doing Stuff Outdoors. Trolling is technique primarily used to catch seatrout. In order to troll w/a kayak a rod holder must be suitably placed. The best locations for a rod holder is directly in front of the cockpit. This location allows the paddler to see the strike as well as detect if the lure has hung weeds. The speeds nessecary to troll most lures is between 3 to 3.5 mph.
This is normally a very leisurely touring pace for most kayakers. Trolling also has its own unique advantages. The first of these is the ability to cover water. Seatrout for most of the year are spread out fairly evenly across the flats. Cold weather or a abundance of bait may concentrate trout in a specific area for brief periods, but these conditions are usually temporary. Another advantage of trolling is simply the ability to be fishing all the time.
If you do not fish until you have reached a desired spot you have wasted all of the travel time not fishing. In a power boat this travel time, may be insignifigant, in a kayak however, it is not. In the Banana River Manatee Sanctuary I frequently travel 4 or more miles to my favorite spots to fish. By trolling on the way I increase my fishing time signifigantly. Finally trolling offers the advantage of being able to non sight fish. By this I mean that sight fishing requires calm to near calm conditions in order to see the fish.
The kayak troller is largely unconcerned w/wind. This ability to fish in the wind allows me to sight fish in the morning calm and then switch to trolling in the afternoon once the wind has gotten up. The lures trolled in flats fishing depend on the depth. Minnow plugs such as the Yo-Zuri L-Minnow are an excellent choice for water over 4 feet deep. In shallower water the best choice is a weedless spoon like a Johnson or Hopkins.